Research workbench
Ternary complex of aflatoxin B1 adduct modified DNA (AFB1-N7-gua) with DNA polymerase IV and incoming datp
Analyse Ternary complex of aflatoxin B1 adduct modified DNA (AFB1-N7-gua) with DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PW4
- Type
- protein + DNA
- Length
- 370 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase IV; DNA (5'-D(*TP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)- 3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- DTP, AFN, CA
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase IV (EC 2.7.7.7) | protein | 342 | 44% helix, 23% strand | Q97W02 |
| B | DNA (5'-D(*TP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)- 3') | dna | 15 | — | — |
| C | DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3') | dna | 13 | — | — |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A, B
- AFN · 8,9-dihydro-9-hydroxy-aflatoxin B1 · ligand · chains A, B, C
- CA · Calcium ion · metal · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.77 | 0.80 | 68 | DTP, CA, AFN |
| 2 | 424 | 0.73 | 0.83 | 36 | empty |
| 3 | 52 | 0.29 | 0.76 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–B · 816 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 544 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- A–C · 539 Ų buried · 14 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3PW4 · Ternary complex of Aflatoxin B1 Adduct modified DNA (AFB1-N7-Gua) with DNA Polymerase IV… · the same entry in another collection · chain A against A, TM-score 1.00
- Q97W02 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q97W02) · a predicted model of the same protein · chain A against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q97W02
- Elsewhere: RCSB PDB 3PW4 · PDBe 3PW4 · UniProt Q97W02
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.